Cytoscape is an Open Source software project for integrating biomolecular interaction networks with genome-scale expression data and other molecular states into a unified conceptual framework. The software is built and maintained by a cross-disciplinary and cross-institutional collaboration, expanding over the past several years to include groups at the University of California San Diego, the Institute for Systems Biology, and the Computational Biology Center at Memorial Sloan-Kettering Cancer Center. We propose an aggressive program of research and development for expanding the current code base, including improvements to the Cytoscape core architecture and user interface; construction of a data services layer with direct access to multiple biological databases hosted on the Internet; and, to extend Cytoscape's applicability to a broader biological research community, a substantial increase in the number of publicly available plug-in analyses. Equally as important, we plan rigorous measures to bolster and maintain existing features, including a library of software unit tests; design rules of thumb; timely and thorough documentation and release of new versions; and community open-source support. In so doing, Cytoscape promises to become an integrated and accessible entry-point into the large amount of molecular interaction data now being generated. Moreover, through computational modeling of biomolecular interaction networks, Cytoscape will be a key enabling technology towards one of the ultimate goals of systems biology: to draft and map the complete high-level 'wiring diagram' of molecular interactions driving cellular physiology, evolution, and disease; and to interface this wiring diagram to lower level physico-chemical models of the cell.